Commit a8246ca8 authored by Tom Harrop's avatar Tom Harrop
Browse files

add pod5

(cherry picked from commit aa2b3813)
parent 21e7a222
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+2 −0
Original line number Diff line number Diff line
@@ -361,6 +361,7 @@
    <datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>
    <datatype extension="fast5.tar.bz2" type="galaxy.datatypes.binary:Fast5ArchiveBz2" display_in_upload="true"/>
    <datatype extension="fast5.tar.xz" type="galaxy.datatypes.binary:Fast5ArchiveXz" display_in_upload="true"/>
    <datatype extension="pod5" type="galaxy.datatypes.binary:Pod5" display_in_upload="true"/>
    <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
    <datatype extension="percin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
    <datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true"/>
@@ -1079,6 +1080,7 @@
    <sniffer type="galaxy.datatypes.binary:Fast5ArchiveXz"/>
    <sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>
    <sniffer type="galaxy.datatypes.binary:Fast5Archive"/>
    <sniffer type="galaxy.datatypes.binary:Pod5"/>
    <sniffer type="galaxy.datatypes.binary:Meryldb" />
    <sniffer type="galaxy.datatypes.binary:Bref3" />
    <sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>
+29 −0
Original line number Diff line number Diff line
@@ -3759,6 +3759,35 @@ class Fast5ArchiveBz2(Fast5Archive):
        return Fast5Archive.sniff(self, filename)


class Pod5(Binary):
    """
    Class describing a Pod5 file

    >>> from galaxy.datatypes.sniff import get_test_fname
    >>> fname = get_test_fname('test.pod5')
    >>> Pod5().sniff(fname)
    True
    """

    file_ext = "pod5"

    def sniff(self, filename: str) -> bool:
        expected_signature = bytes(
            [0x8B, 0x50, 0x4F, 0x44, 0x0D, 0x0A, 0x1A, 0x0A]
        )
        try:
            with open(filename, "rb") as f:
                first_8_bytes = f.read(8)
                f.seek(-8, 2)
                last_8_bytes = f.read(8)
                return (
                    first_8_bytes == expected_signature
                    and last_8_bytes == expected_signature
                )
        except Exception:
            return False


class SearchGuiArchive(CompressedArchive):
    """Class describing a SearchGUI archive"""

+79.1 KiB

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